Contacts of the helix formed by residues 172 - 184 (chain D) in PDB entry 2YWB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 172 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 6.0 0.2 - - - +
253B GLU* 6.1 1.1 - - - +
407B ASP* 3.0 34.7 + - - -
411B SER* 3.7 17.5 - - - +
414B ARG* 6.6 0.2 - - - -
115D GLY 5.6 1.1 - - - +
116D LEU* 4.0 30.5 - - + +
117D GLU 3.0 20.0 + - - +
119D GLU 2.8 27.3 + - - +
120D VAL* 4.6 12.3 - - + -
121D GLN 5.1 0.8 + - - +
170D THR* 3.2 3.4 - - + +
171D PRO* 1.3 80.1 - - + +
173D GLY* 1.3 63.1 + - - +
174D MET 3.2 2.5 - - - -
175D GLN* 3.2 20.9 + - + +
176D ILE* 3.3 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D PRO* 3.2 31.1 - - - +
170D THR* 2.7 27.4 + - - +
171D PRO 3.1 0.2 - - - -
172D LYS* 1.3 75.7 - - - +
174D MET* 1.3 64.3 + - - +
176D ILE* 3.1 7.7 + - - +
177D LEU* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ASP* 5.7 2.5 - - + -
374B THR* 3.9 22.5 - - + +
18D ARG* 3.1 57.2 - - - +
21D GLU* 3.2 31.6 - - + +
22D LEU* 3.5 16.6 - - + +
165D PRO 3.9 3.4 + - - +
170D THR 4.6 0.4 + - - -
171D PRO 4.3 7.0 + - - +
172D LYS 3.2 0.6 - - - -
173D GLY* 1.3 76.4 - - - +
175D GLN* 1.3 58.2 + - - +
177D LEU* 3.3 7.0 + - - +
178D GLU* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLU* 3.2 55.4 + - - +
374B THR* 4.1 21.3 + - + +
375B LEU* 5.3 1.9 - - - +
114D ARG 4.1 3.5 + - - +
116D LEU* 3.8 18.8 - - + -
172D LYS* 3.2 16.7 + - + +
174D MET* 1.3 77.0 - - - +
176D ILE* 1.3 60.6 + - - +
178D GLU* 3.8 17.0 - - - +
179D ASN* 2.9 56.1 + - - -
182D GLU* 4.8 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 5.6 3.4 - - + -
112D LEU* 4.0 33.0 - - + +
113D PHE* 4.1 7.6 - - + -
116D LEU* 3.4 33.2 - - + -
120D VAL* 5.1 3.1 - - + -
161D VAL* 5.3 3.6 - - + -
163D PHE* 3.8 33.0 - - + -
165D PRO* 4.4 12.1 - - + -
170D THR* 4.8 4.5 - - + -
172D LYS 3.3 8.1 + - - +
173D GLY* 3.1 14.3 + - - +
175D GLN* 1.3 75.4 - - - +
177D LEU* 1.3 67.3 + - + +
179D ASN* 3.0 18.3 + - - +
180D PHE* 3.0 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE* 5.5 5.2 - - + +
18D ARG* 3.7 32.5 - - + -
19D LEU* 5.5 6.9 - - + +
22D LEU* 4.2 11.0 - - + -
47D ILE* 4.7 13.2 - - + -
75D LEU* 3.6 26.9 - - + -
77D ILE* 4.9 4.5 - - + -
165D PRO* 4.0 28.9 - - + +
166D GLU* 4.2 8.1 - - + -
173D GLY 3.0 16.4 + - - +
174D MET* 3.3 10.7 + - - +
176D ILE* 1.3 76.1 - - + +
178D GLU* 1.3 56.9 + - - +
180D PHE* 3.4 6.9 + - + +
181D LEU* 3.1 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ALA* 4.4 6.2 - - + +
261B LEU* 5.3 0.5 - - - +
372B PRO* 3.5 23.6 - - - +
374B THR* 4.5 10.1 - - + +
22D LEU* 3.8 14.6 - - + +
174D MET 2.9 17.5 + - - +
175D GLN* 3.5 22.9 - - - +
177D LEU* 1.3 75.6 - - - +
179D ASN* 1.3 59.7 + - - +
181D LEU* 3.3 3.0 + - - +
182D GLU* 2.4 53.8 + - - +
188D ARG* 3.0 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D PRO 3.3 20.2 - - - +
112D LEU* 3.1 22.7 + - - +
114D ARG* 2.9 34.0 + - - +
116D LEU* 3.7 8.9 - - - +
175D GLN* 2.9 41.4 + - - +
176D ILE 3.0 6.0 + - - +
178D GLU* 1.3 76.2 - - - +
180D PHE* 1.3 57.9 + - - +
182D GLU* 3.4 14.2 + - - +
183D LEU* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ALA* 3.9 26.5 - - + -
46D LEU 3.8 8.7 - - - -
47D ILE* 4.0 12.3 - - + -
73D PRO* 4.0 4.3 - - + -
74D LEU 3.4 44.9 - - - -
75D LEU* 3.6 35.7 - - + -
112D LEU* 4.2 10.5 - - + +
157D ARG 4.6 0.7 - - - -
159D TYR* 4.4 19.7 - + - -
176D ILE 3.0 12.1 + - - +
177D LEU* 3.6 8.7 - - + +
179D ASN* 1.3 76.0 - - - +
181D LEU* 1.3 69.0 + - + +
183D LEU* 3.0 6.6 + - + +
184D ALA* 2.7 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D VAL* 3.9 18.2 - - + -
19D LEU* 3.9 18.8 - - + -
22D LEU* 3.6 35.2 - - + +
24D ALA* 3.9 17.9 - - + -
177D LEU 3.1 18.3 + - - +
178D GLU* 3.8 4.7 - - - +
180D PHE* 1.3 88.7 - - + +
182D GLU* 1.3 61.4 + - - +
184D ALA* 3.6 0.4 + - - -
185D GLY 3.1 2.3 + - - -
186D VAL* 2.8 57.0 + - + +
188D ARG* 3.8 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLU 4.8 0.7 - - - +
256B GLY* 3.1 29.8 - - - +
257B ALA* 3.4 14.5 + - - +
260B ALA* 3.8 19.1 - - + +
114D ARG* 5.0 4.5 + - - -
175D GLN* 4.8 3.0 + - - -
178D GLU* 2.4 52.4 + - - +
179D ASN* 3.6 14.1 - - - +
181D LEU* 1.3 76.1 - - - +
183D LEU* 1.3 65.4 + - + +
185D GLY* 3.2 12.6 + - - -
186D VAL 5.7 0.2 - - - -
188D ARG* 3.7 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D PRO* 3.2 37.2 - - + +
112D LEU* 3.9 13.7 - - + +
114D ARG* 6.3 0.2 - - - -
156D GLY 5.4 3.1 - - - +
159D TYR* 3.4 39.5 - - + +
179D ASN 2.9 25.9 + - - +
180D PHE* 3.4 11.0 - - + +
182D GLU* 1.3 75.0 - - + +
184D ALA* 1.3 57.7 + - - +
185D GLY* 2.9 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLN* 3.9 11.6 - - - +
45D ALA* 3.8 18.2 - - + -
73D PRO* 3.3 38.9 - - + +
180D PHE* 2.7 25.8 + - + +
183D LEU* 1.3 71.3 - - - +
185D GLY* 1.3 64.4 + - - +
186D VAL* 3.1 7.8 + - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il